You said: "Duties were collected where the goods were landed, and there were customs houses in any port where imports arrived."
How would they arrive in the places like these?
Mississippi and Ohio Rivers are two ways. The Great Lakes are another. I'd be willing to wager that not much in the way of tariffs were collected.
Knoxville looks out of place. Here's what wikipedia has to say about Knoxville's Old Custom House:
The U.S. Customs House was built at a time when Congress was petitioned by cities across the country to provide courtrooms and post offices. Congress was reluctant to provide funding for buildings that only contained judicial and postal functions, so the title Customs House was added. Congress was viewed as more agreeable to providing construction funding if excise taxes collected from foreign imports were linked to projects, since taxes generated revenue.
That may also be true of Cairo and Sandusky.